Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,487,041	C→T	T275I (ACC→ATC)	lptF →	lipopolysaccharide export ABC permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,487,041	0	C	T	100.0%	106.1 / NA	32	T275I (ACC→ATC)	lptF	lipopolysaccharide export ABC permease
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (16/16);  total (16/16)

ATCAGGCGATCATTGGTCACCAGGCGGTGGCGCTCGACCCGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCACCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACTTTTCTTCCTGATCCAGACCTCCCTGAAATCGAAC  >  NC_000913/4486906‑4487174                                                                                                                                        |                                                                                                                                      aTCAGGCGATCATTGGTCACCAGGCGGTGGCGCTCGACCCGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCgt                                                                                                                                    >  1:229739/1‑139 (MQ=255)                  cACCAGGCGGTGGCGCTCGACCCGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTa                                                                                                                   >  2:36180/1‑139 (MQ=255)                     cAGGCGGTGGCGCTCGACCCGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATgg                                                                                                                >  2:172588/1‑139 (MQ=255)                        gCGGTGGCGCTCGACCCGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTatga                                                                                                                            >  2:302963/1‑124 (MQ=255)                        gCGGTGGCGCTCGACCCGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTatga                                                                                                                            <  1:302963/124‑1 (MQ=255)                                   cGACCCGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGc                                                                                                  <  2:229739/139‑1 (MQ=255)                                             gATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGTGTGGTTAAcc                                                                                        <  2:698953/139‑1 (MQ=255)                                                    aCCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGTACTTATGGTCGTACCGCTGAGCGTGGTTAAcc                                                                                        <  1:243241/132‑1 (MQ=255)                                                    aCCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGTACTTATGGTCGTACCGCTGAGCGTGGTTAAcc                                                                                        >  2:243241/1‑132 (MQ=255)                                                    aCCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCa                                                                                 <  1:297641/139‑1 (MQ=255)                                                    aCCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCa                                                                                 >  1:577945/1‑139 (MQ=255)                                                            gACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGAGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGAcgcg                                                                         <  1:418395/139‑1 (MQ=255)                                                                                   tGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAAcc                                                                                        >  2:63888/1‑101 (MQ=255)                                                                                   tGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAAcc                                                                                        <  1:63888/101‑1 (MQ=255)                                                                                   tGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCAtg                                                  >  1:696113/1‑139 (MQ=255)                                                                                        ccGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATgctgct                                             <  2:127439/139‑1 (MQ=255)                                                                                           aTCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGt                                                                                             >  2:185451/1‑88 (MQ=255)                                                                                           aTCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGt                                                                                             <  1:185451/88‑1 (MQ=255)                                                                                           aTCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGAcgcg                                                                         >  1:145650/1‑108 (MQ=255)                                                                                           aTCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGAcgcg                                                                         <  2:145650/108‑1 (MQ=255)                                                                                           aTCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCAtgct                                                >  2:221312/1‑133 (MQ=255)                                                                                           aTCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCAtgct                                                <  1:221312/133‑1 (MQ=255)                                                                                                    gcgcAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACtttt                                 <  1:172588/139‑1 (MQ=255)                                                                                                     cgcAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACTTttc                                >  2:400450/1‑139 (MQ=255)                                                                                                                  tggtgTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGt                                           <  2:246575/111‑1 (MQ=255)                                                                                                                  tgGTGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGt                                           >  1:246575/1‑115 (MQ=255)                                                                                                                    gCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAg                                                                                                   >  1:692763/1‑57 (MQ=255)                                                                                                                    gCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAg                                                                                                   <  2:692763/57‑1 (MQ=255)                                                                                                                       tATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCAtgct                                                <  1:674343/105‑1 (MQ=255)                                                                                                                       tATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCAtgct                                                >  2:674343/1‑105 (MQ=255)                                                                                                                         tCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACTTTTCTTCCTGATCCAGACCTCCCt            >  1:132079/1‑139 (MQ=255)                                                                                                                                   aTTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACTTTTCTTCCTGATCCAGACCTCCCTGAAATCGAAc  <  1:36180/139‑1 (MQ=255)                                                                                                                                        |                                                                                                                                      ATCAGGCGATCATTGGTCACCAGGCGGTGGCGCTCGACCCGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCACCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACTTTTCTTCCTGATCCAGACCTCCCTGAAATCGAAC  >  NC_000913/4486906‑4487174

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑